Np mrd loader

Showing NP-Card for Procyanidin (NP0047086)

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Record Information
Version2.0
Created at2022-03-17 20:34:24 UTC
Updated at2022-03-17 20:34:24 UTC
NP-MRD IDNP0047086
Secondary Accession NumbersNone
Natural Product Identification
Common NameProcyanidin
Description Procyanidin is found in Lathyrus pratensis, Lotus pedunculatus, Patersonia fragilis, Phoenix sylvestris, Pinus brutia, Pinus halepensis, Pseudotsuga menziesii, Theobroma cacao and Vitis amurensis.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0047086 (Procyanidin)


  Mrv1533004171517402D          

 43 48  0  0  0  0            999 V2000
   -0.0980   -4.3942    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0980   -3.5692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8125   -3.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3768   -3.8822    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.2233   -6.2080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5055   -6.9832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for NP0047086 (Procyanidin)

Download
3D SDF for NP0047086 (Procyanidin)

  Mrv1533004171517402D          

 43 48  0  0  0  0            999 V2000
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   -2.7196   -3.3935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.0623   -2.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3105   -1.4975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8408   -0.8656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4980   -1.3543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2158   -0.5790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0980   -1.9192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0047086

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(O)C(OC2CC3=C(O)C=C(O)C=C3OC2C2=CC=C(O)C(O)=C2)(OC2=CC(O)=CC(O)=C12)C1=CC=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O13/c31-14-7-19(35)16-11-25(28(41-23(16)9-14)12-1-3-17(33)20(36)5-12)43-30(13-2-4-18(34)21(37)6-13)29(40)27(39)26-22(38)8-15(32)10-24(26)42-30/h1-10,25,27-29,31-40H,11H2

> <INCHI_KEY>
HGVVOUNEGQIPMS-UHFFFAOYSA-N

> <FORMULA>
C30H26O13

> <MOLECULAR_WEIGHT>
594.525

> <EXACT_MASS>
594.137340897

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
57.25404241232627

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3,4-dihydroxyphenyl)-2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol

> <ALOGPS_LOGP>
2.27

> <JCHEM_LOGP>
3.643237414333333

> <ALOGPS_LOGS>
-3.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.068989952059827

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.63804757793863

> <JCHEM_PKA_STRONGEST_BASIC>
-4.728418614261462

> <JCHEM_POLAR_SURFACE_AREA>
229.98999999999995

> <JCHEM_REFRACTIVITY>
147.1641

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3,4-dihydroxyphenyl)-2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-3,4-dihydro-1-benzopyran-3,4,5,7-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0047086 (Procyanidin)
Download
PDB for NP0047086 (Procyanidin)
HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0      -0.183  -8.203   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.183  -6.663   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.517  -5.893   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.678  -7.424   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.517  -4.353   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.033  -4.620   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -3.560  -6.067   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.570  -7.247   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.097  -8.694   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.107  -9.874   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.590  -9.606   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.634 -11.321   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.150 -11.588   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -4.677 -13.035   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -5.140 -10.409   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.613  -8.961   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -5.603  -7.782   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -5.077  -6.335   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.066  -5.155   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.583  -5.422   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -8.573  -4.243   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -8.046  -2.795   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -9.036  -1.616   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -6.530  -2.528   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -6.003  -1.081   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -5.540  -3.708   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.183  -3.583   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.151  -4.353   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.484  -3.583   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       3.818  -4.353   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       5.152  -3.583   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       3.818  -5.893   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.484  -6.663   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.484  -8.203   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.151  -5.893   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.043  -2.905   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -3.560  -2.638   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -4.087  -1.191   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.097  -0.011   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -3.623   1.436   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.580  -0.279   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -0.590   0.901   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -1.053  -1.726   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   27   36                                             
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    9   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17    7   19                                                  
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19                                                       
CONECT   27    5   28                                                       
CONECT   28   27   29   35                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    2   28                                                  
CONECT   36    5   37   43                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   36                                                       
MASTER        0    0    0    0    0    0    0    0   43    0   96    0
END

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3D PDB for NP0047086 (Procyanidin)
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SMILES for NP0047086 (Procyanidin)
OC1C(O)C(OC2CC3=C(O)C=C(O)C=C3OC2C2=CC=C(O)C(O)=C2)(OC2=CC(O)=CC(O)=C12)C1=CC=C(O)C(O)=C1
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INCHI for NP0047086 (Procyanidin)
InChI=1S/C30H26O13/c31-14-7-19(35)16-11-25(28(41-23(16)9-14)12-1-3-17(33)20(36)5-12)43-30(13-2-4-18(34)21(37)6-13)29(40)27(39)26-22(38)8-15(32)10-24(26)42-30/h1-10,25,27-29,31-40H,11H2
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View in JSmol
Synonyms
ValueSource
Procyanidin, (2R-(2alpha,3alpha,4alpha(2'r*,3's*)))-isomerMeSH
Procyanidin, (2R-(2alpha,3beta,4beta(2R*,3R*)))-isomerMeSH
ProcyanidineMeSH
Procyanidin type aMeSH
Type a procyanidinMeSH
a-Type procyanidinMeSH
Epicatechin-4alpha,8-epicatechinMeSH
Chemical FormulaC30H26O13
Average Mass594.5250 Da
Monoisotopic Mass594.13734 Da
IUPAC Name2-(3,4-dihydroxyphenyl)-2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-3,4-dihydro-2H-1-benzopyran-3,4,5,7-tetrol
Traditional Name2-(3,4-dihydroxyphenyl)-2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-3,4-dihydro-1-benzopyran-3,4,5,7-tetrol
CAS Registry NumberNot Available
SMILES
OC1C(O)C(OC2CC3=C(O)C=C(O)C=C3OC2C2=CC=C(O)C(O)=C2)(OC2=CC(O)=CC(O)=C12)C1=CC=C(O)C(O)=C1
InChI Identifier
InChI=1S/C30H26O13/c31-14-7-19(35)16-11-25(28(41-23(16)9-14)12-1-3-17(33)20(36)5-12)43-30(13-2-4-18(34)21(37)6-13)29(40)27(39)26-22(38)8-15(32)10-24(26)42-30/h1-10,25,27-29,31-40H,11H2
InChI KeyHGVVOUNEGQIPMS-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Annona muricataFooDB
Ginkgo bilobaFooDB
Lathyrus pratensisLOTUS Database
Lotus pedunculatusLOTUS Database
Patersonia fragilisLOTUS Database
Phoenix sylvestrisLOTUS Database
Pinus brutiaLOTUS Database
Pinus halepensisLOTUS Database
Pseudotsuga menziesiiLOTUS Database
Syzygium aromaticumFooDB
Theobroma cacaoLOTUS Database
Vitis amurensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavans  
Direct ParentCatechins  
Alternative Parents
Substituents
  • Catechin
    • 

  • Hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • 5-hydroxyflavonoid
    • 

  • 4-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 3-hydroxyflavonoid
    • 

  • 3'-hydroxyflavonoid
    • 

  • 1-benzopyran
    • 

  • Benzopyran
    • 

  • Chromane
    • 

  • Benzylether
    • 

  • Catechol
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • Alkyl aryl ether
    • 

  • Ketal
    • 

  • Phenol
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Benzenoid
    • 

  • Monocyclic benzene moiety
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Ether
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.27ALOGPS
logP3.64ChemAxon
logS-3.5ALOGPS
pKa (Strongest Acidic)8.64ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area229.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity147.16 m³·mol⁻¹ChemAxon
Polarizability57.25 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB007223  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkProcyanidin  
METLIN IDNot Available
PubChem Compound107876  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available